retFatMatrix: retFatMatrix

In flagme: Analysis of Metabolomics GC/MS Data

Description

Build a fat data matrix

Usage

retFatMatrix(object, data, minFilter = 1)

Arguments

object	peakDataset object
data	a gatherInfo() object
minFilter	the minimum number for a feature to be returned in the data matrix

Details

This function allows to extract the data from an object created using gatherInfo and build a data matrix using the area of the deconvoluted and aligned peaks. The row are the samples while the column represent the different peaks.

Value

A fat data matrix containing the area of the deconvoluted and aligned peaks. The row are the samples while the column represent the different peaks

Author(s)

Riccardo Romoli [e-mail]

See Also

gatherInfo

Examples

require(gcspikelite)
# paths and files
gcmsPath <- paste(find.package("gcspikelite"), "data", sep = "/")
cdfFiles <- dir(gcmsPath,"CDF",full=TRUE)
# read data, peak detection results
pd <- peaksDataset(cdfFiles[1:2], mz=seq(50,550),
                   rtrange=c(7.5,8.5))
pd <- addXCMSPeaks(files=cdfFiles[1:2], object=pd,
                   peakPicking=c('mF'), snthresh=3, fwhm=4,
                   step=1, steps=2, mzdiff=0.5)
ma <- multipleAlignment(pd = pd, group = c(1,1),
                        filterMin = 1, metric = 2, type = 2)
outList <- gatherInfo(pd, ma)
mtxD <- retFatMatrix(object = pd, data = outList, minFilter = 1)

flagme documentation built on Nov. 8, 2020, 5:24 p.m.